BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081243.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,970,445 number of mapped reads = 1,740,111 (88.31%) number of supplementary alignments = 18,723 (0.95%) number of secondary alignments = 0 number of mapped bases = 112,890,826 bp number of sequenced bases = 112,847,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,178 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6518 >>>>>>> ACTG content number of A's = 32,552,558 bp (28.85%) number of C's = 21,554,414 bp (19.1%) number of T's = 34,813,406 bp (30.85%) number of G's = 23,913,131 bp (21.19%) number of N's = 13,992 bp (0.01%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,015,838 number of insertions = 8,580 mapped reads with insertion percentage = 0.49% number of deletions = 26,428 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.21% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.285X There is a 3% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11822390 0.04743173739173954 0.3980111260076313 chr2 243199373 7139423 0.02935625578278115 0.28807291369409865 chr3 198022430 7956186 0.04017820607493808 0.2376551135510262 chr4 191154276 4995859 0.026135219700761495 0.19702890269231466 chr5 180915260 5848132 0.03232525548148896 0.2113019834155507 chr6 171115067 8286440 0.04842612719778791 0.27207936394008103 chr7 159138663 7244587 0.045523739256248495 0.3318817613581758 chr8 146364022 7530237 0.051448688667492345 0.4945370011400836 chr9 141213431 3034913 0.021491673833772935 0.21218602099498518 chr10 135534747 3752977 0.027690146498004678 0.263296634940918 chr11 135006516 6798681 0.05035816937902464 0.3645596453644037 chr12 133851895 3629320 0.027114446157075325 0.19322590477312357 chr13 115169878 4157306 0.03609716422552779 0.22581140963724206 chr14 107349540 4411164 0.04109159666636671 0.24197934008760386 chr15 102531392 2047547 0.01996995222692383 0.1740746723642854 chr16 90354753 3662304 0.040532499712549706 0.24240260719455742 chr17 81195210 1625704 0.020022166332225755 0.18457679945706393 chr18 78077248 2785643 0.035678037730018354 0.3499651188951934 chr19 59128983 2311820 0.039097915822431786 0.330733804891683 chr20 63025520 2992101 0.047474435752374596 0.2582569927262308 chr21 48129895 1823541 0.03788790729753306 0.2358395012316689 chr22 51304566 765761 0.014925786527460343 0.14056583593312028 chrMT 16571 13504 0.8149176271800133 1.0777888900853454 chrX 155270560 7959245 0.05126049007616125 0.27961374778684533 chrY 59373566 296041 0.0049860741057729295 0.09738524960886795